Variant report

Variant	rs12230540
Chromosome Location	chr12:120631169-120631170
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:120628864..120642103-chr12:120725347..120732286,54	K562	blood:
2	chr12:120630041..120632673-chr12:121124063..121125965,2	MCF-7	breast:
3	chr12:120628211..120641965-chr12:120660551..120674110,39	K562	blood:
4	chr12:120532676..120534785-chr12:120629802..120632367,2	K562	blood:
5	chr12:120551826..120556882-chr12:120630846..120640383,26	K562	blood:
6	chr12:120626707..120642605-chr12:120719450..120732919,96	MCF-7	breast:
7	chr12:120609315..120613090-chr12:120629973..120633453,5	K562	blood:
8	chr12:120629843..120633670-chr12:120702168..120705891,5	K562	blood:
9	chr12:120581778..120584149-chr12:120629758..120631422,2	K562	blood:
10	chr12:120631139..120640506-chr12:120724902..120734482,54	K562	blood:
11	chr12:120552488..120558210-chr12:120630092..120634088,8	MCF-7	breast:
12	chr12:120552161..120556177-chr12:120630368..120635589,11	K562	blood:

No data

Variant related genes	Relation type
ENSG00000110917	Chromatin interaction
ENSG00000202538	Chromatin interaction
ENSG00000263913	Chromatin interaction
ENSG00000123009	Chromatin interaction
ENSG00000089159	Chromatin interaction
ENSG00000111737	Chromatin interaction
ENSG00000200795	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10774543	0.89[EUR][1000 genomes]
rs12308065	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3956837	0.95[EUR][1000 genomes]
rs4766959	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6490287	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7960843	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7968689	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3525916	chr12:120345352-120665045	Bivalent Enhancer Genic enhancers Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
2	esv3525917	chr12:120345352-120665045	Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
3	nsv899555	chr12:120519124-120840522	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	499 gene(s)	inside rSNPs	diseases
4	nsv519657	chr12:120533696-120676090	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
5	nsv560433	chr12:120533696-120676090	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
6	nsv832530	chr12:120586069-120758175	Flanking Active TSS Strong transcription Enhancers Genic enhancers Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	484 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:120564400-120631800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr12:120594200-120631600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr12:120621600-120631600	Weak transcription	Right Atrium	heart
4	chr12:120622400-120631400	Weak transcription	Fetal Heart	heart
5	chr12:120622600-120631400	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr12:120624800-120631400	Weak transcription	Fetal Brain Male	brain
7	chr12:120624800-120631600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr12:120625000-120631400	Weak transcription	Brain Substantia Nigra	brain
9	chr12:120625600-120631600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr12:120625600-120631600	Weak transcription	Fetal Kidney	kidney
11	chr12:120625800-120631400	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr12:120625800-120631400	Weak transcription	HUVEC	blood vessel
13	chr12:120626000-120631400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr12:120626000-120631400	Weak transcription	Brain Cingulate Gyrus	brain
15	chr12:120626000-120631400	Weak transcription	HSMMtube	muscle
16	chr12:120626200-120631200	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr12:120626200-120631400	Weak transcription	NHDF-Ad	bronchial
18	chr12:120626400-120631200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr12:120627000-120631400	Weak transcription	Brain Anterior Caudate	brain
20	chr12:120627200-120631200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr12:120627600-120631400	Weak transcription	Primary neutrophils fromperipheralblood	blood
22	chr12:120627600-120631400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr12:120627800-120631200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr12:120627800-120631400	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr12:120627800-120631400	Weak transcription	Colon Smooth Muscle	Colon
26	chr12:120627800-120631400	Weak transcription	Ovary	ovary
27	chr12:120627800-120631600	Weak transcription	Brain Angular Gyrus	brain
28	chr12:120628200-120631200	Weak transcription	Duodenum Mucosa	Duodenum
29	chr12:120628200-120631200	Weak transcription	Fetal Lung	lung
30	chr12:120628200-120631400	Weak transcription	Fetal Intestine Large	intestine
31	chr12:120628200-120631400	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr12:120628200-120631600	Weak transcription	Esophagus	oesophagus
33	chr12:120628400-120631200	Weak transcription	Primary monocytes fromperipheralblood	blood
34	chr12:120628400-120631200	Weak transcription	Spleen	Spleen
35	chr12:120628400-120631400	Weak transcription	Primary hematopoietic stem cells	blood
36	chr12:120628400-120631400	Weak transcription	Brain Hippocampus Middle	brain
37	chr12:120628400-120631400	Weak transcription	Colonic Mucosa	Colon
38	chr12:120628400-120631400	Weak transcription	Rectal Smooth Muscle	rectum
39	chr12:120628400-120631600	Weak transcription	Lung	lung
40	chr12:120628600-120631200	Weak transcription	Brain Germinal Matrix	brain
41	chr12:120628600-120631600	Weak transcription	Gastric	stomach
42	chr12:120628800-120631400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr12:120629000-120631200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr12:120629000-120631200	Weak transcription	Placenta	Placenta
45	chr12:120629000-120631200	Weak transcription	Left Ventricle	heart
46	chr12:120629000-120631400	Weak transcription	Thymus	Thymus
47	chr12:120629000-120631600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr12:120629000-120631600	Weak transcription	Aorta	Aorta
49	chr12:120629200-120631200	Weak transcription	Fetal Intestine Small	intestine
50	chr12:120629200-120631400	Weak transcription	Fetal Brain Female	brain

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